\Header{visualiseQualityParameters}{Graphical representation of quality parameters}
\keyword{hplot}{visualiseQualityParameters}
\begin{Description}\relax
Graphical representation of quality parameters
\end{Description}
\begin{Usage}
\begin{verbatim}visualiseQualityParameters(qualityParameters, savePath, fileName="visualiseQualityParametersOutput.pdf", width=25, height=25, plotOutput="pdf")\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{qualityParameters}] \code{data.frame}; required; 
contained in the return value of
\code{\Link{qualityParameters}} 
\item[\code{fileName}] character string; required;
default: "visualiseQualityParametersOutput.pdf" 
\item[\code{savePath}] character string; optional; default: missing
\item[\code{width}] graphics window width
\item[\code{height}] graphics window height
\item[\code{plotOutput}] character string; required; either "screen", "pdf"
or "win.metafile"; default: "pdf"
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
For details on the specific parameters
see \code{\Link{qualityParameters}}.
Lines are only used for easier
detection of outliers. The ordering
of the hybridisation is somehow arbitrary,
and only reflects the (initial) ordering. 
The "correlation" line for example
graphically represents the correlation
coefficients calculated between the
green and red channel for each hybridisation.
The horizontal blue line is drawn
at the height of one. The function
\code{\Link{qualityDiagnostics}} calls
\code{visualiseQualityParameters}.
\end{Details}
\begin{Value}
A graphical representation of quality parameters.
\code{\Link{qualityDiagnostics}} does call
\code{visualiseQualityParameters}
\end{Value}
\begin{Author}\relax
Andreas Buness <a.buness@dkfz.de>
\end{Author}
\begin{SeeAlso}\relax
\code{\Link{qualityParameters}};
\code{\Link{qualityDiagnostics}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
        \end{ExampleCode}
\end{Examples}

